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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAGgtaactgcactgagcttctttatggatactcaggtgcttcccagttttgtataaataataaattgtgctggattgctctttgtag

Basic information

species Zea mays
transcript GRMZM2G160458_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160458_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g37870.1 (Oryza sativa), 5'ss of exon 6
ATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAGgtaactgcactgagcttctttatggata-----ctcaggtgcttcccagttttgtataaataataaattgtgctggattgctctttgtag
||||| |||||||||||||||||||| || ||||||||||| |||||||| || ||||||||| |||||||||  || |  ||||||| | || |||      |    || |||| ||||| || | | |      ||| | | ||     || |||||
ATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGACAAGATGACACTTGTTGAGgtaaaggcgcatagcttctatttgtataatatttttttatgtttccaagtttagtttcagtt-----ttgagatcgaacttgctgtgtag

upper sequence: GRMZM2G160458_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT1G52930.1 (Arabidopsis thaliana), 5'ss of exon 5
-------------------------------ATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAGgtaactgcactgagcttctttatggatactcaggtgcttcccagttttgtataaataataaattgtgctggattgctctttgtag
                               ||||||||||| |||||||||   |||||| |||  |||||||| |||||||||||||| ||||| |||||   || ||  ||  |    |    |    |   |  |  |     ||  |    | | || || | |  | |  |      ||
TGATGAGCATATATGGTTCCGAAATTACCAGATTTCGGTTCCTCACAATGAGTCAGATAAAATTGCAAAAGGTGGCCTGGATAAAATGACCCTTATCGAGgtttgtggacaaagagttacaaacttttaataatagtctttcgaccatggtttttgattgaaatg-gatacactattgacaacag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|110202290|gb|EC884187.1|EC884187
EST:     AGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAG                         GTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
genomic: AGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAGgtaactgcac ... ctctttgtagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
EST: gi|148946147|gb|EC891441.2|EC891441
EST:     AGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAG                         GTGGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
genomic: AGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAGgtaactgcac ... ctctttgtagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
EST: gi|148996317|gb|EE035601.2|EE035601
EST:     GATTGATAAAGTTTGATAA-GGTGGTCTGGATAAAATGACACTTATTGAG                         GGTGGCCCCCAGGTTCTGTTTGAATCCAATCAAAATATT
genomic: GATTGATAAAGTT-GATAAAGGTGGTCTGGATAAAATGACACTTATTGAGgtaactgcac ... ctctttgtagGTTGGCCCC-AGGTTCTGTTTGAATCCAATCAAAATATT
EST: gi|149070865|gb|EE159274.2|EE159274
EST:     AGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAG                         GTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
genomic: AGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAGgtaactgcac ... ctctttgtagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
EST: gi|110196089|gb|EC877986.1|EC877986
EST:     AGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAG                         GTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
genomic: AGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAGgtaactgcac ... ctctttgtagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
EST: gi|33468119|gb|CF245168.1|CF245168
EST:     AGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAG                         GTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
genomic: AGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAGgtaactgcac ... ctctttgtagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
EST: gi|71429925|gb|DR810975.1|DR810975
EST:     AGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAG                         GTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
genomic: AGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAGgtaactgcac ... ctctttgtagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
EST: gi|211114336|gb|FL479348.1|FL479348
EST:     AGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAG                         GTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
genomic: AGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAGgtaactgcac ... ctctttgtagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
EST: gi|50332850|gb|CO527976.1|CO527976
EST:     AGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAG                         GTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
genomic: AGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAGgtaactgcac ... ctctttgtagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
EST: gi|60347622|gb|DN214595.1|DN214595
EST:     AGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAG                         GTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
genomic: AGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAGgtaactgcac ... ctctttgtagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
EST: gi|78089923|gb|DV518297.1|DV518297
EST:     AGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAG                         GTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
genomic: AGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAGgtaactgcac ... ctctttgtagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
EST: gi|86469691|gb|DY236061.1|DY236061
EST:     AGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAG                         GTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
genomic: AGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAGgtaactgcac ... ctctttgtagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

ATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAGgtaactgcac ... ctctttgtagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTTGGTGGTCCTACATGGTATGAGAACCCATACTACATTTCCCCCAATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 48

ATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAGgtaactgcac ... ctctttgtagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTTGGTGGTCCTACATGGTATGAGAACCCATACTACATTTCCCCCAATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 44

ATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAGgtaactgcac ... ctctttgtagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTTGGTGGTCCTACATGGTATGAGAACCCATACTACATTTCCCCCAATCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 18

ATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAGgtaactgcac ... ctctttgtagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTTGGTGGTCCTACATGGTATGAGAACCCATACTACATTTCCCCCAATCAG